Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

Abstract

BackgroundImprovement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids.ResultsWe sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol. The genome is comprised of highly methylated repetitive sequence, which does not significantly change under silicon starved lipid induction, and data further suggests the primary role of DNA methylation is to suppress DNA transposition. Annotation of pivotal glycolytic, lipid metabolism, and carbohydrate degradation processes reveal an expanded enzyme repertoire in C. cryptica that would allow for an increased metabolic capacity toward triacylglycerol production. Identification of previously unidentified genes, including those involved in carbon transport and chitin metabolism, provide potential targets for genetic manipulation of carbon flux to further increase its lipid phenotype. New genetic tools were developed, bringing this organism on a par with other microalgae in terms of genetic manipulation and characterization approaches.ConclusionsFunctional annotation and detailed cross-species comparison of key carbon rich processes in C. cryptica highlights the importance of enzymatic subcellular compartmentation for regulation of carbon flux, which is often overlooked in photosynthetic microeukaryotes. The availability of the genome sequence, as well as advanced genetic manipulation tools enable further development of this organism for deployment in large-scale production systems.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0670-3) contains supplementary material, which is available to authorized users.

Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions

“…In P. infestans and P. sojae , we observed a bimodal distribution pattern of 6mA enriched regions flanking the TSS, but with a clear depletion at the TSS itself and immediately downstream. This pattern resembles 6mA methylation described for the green algae Chlamydomonas 41 . Our comparisons of transcriptome and methylome data suggest that 6mA is negatively correlated with gene expression in the two Phytophthora species.…”

Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin‐based metabolic processes in diatoms

“…Recently, the sequencing of multiple diatom genomes (P. tricornutum, T. pseudonana, and, more recently, Cyclotella cryptica) has provided potential for studies of chitin/chitosan biosynthetic pathways (Armbrust et al, 2004;Bowler et al, 2008;Traller et al, 2016). However, the analysis of biological function, especially for CDA, is largely lacking, and the distinct features of chitin/chitosan in pennate and centric diatoms remain elusive.…”

Systematic and functional analysis of horizontal gene transfer events in diatoms

“…is the first large-scale and systematic approach of HGT detection across all available sequenced 258 diatoms. While some previous studies were based on phylogenetics 7,30 , most relied purely on sequence 259 homology searches 24,25,27 , while it has been shown that the degree of gene similarity does not 260 necessary necessarily reflect phylogenetic relationships 65,66 . Although HGT had been previously 261 predicted in P. multistriata, C. cryptica, T. oceanica and twice in P. tricornutum, only a fraction of HGT 262 genes were confirmed across these studies, going from 6 to 45% ( Figure S12).…”

“…In the early 22 Cretaceous, between 150 and 130 million years ago, diatoms split into the centric and pennate lineage. 23 Several whole-genome sequences of representatives from polar centrics (Thalassiosira pseudonana 23 , 24 Thalassiosira oceanica 24 , Cyclotella cryptica 25 ), araphid pennates (Synedra acus 26 ) and raphid pennates 25 (Phaeodactylum tricornutum 7,27 , Fistulifera solaris 28 , Fragilariopsis cylindrus 29 , Pseudo-nitzschia 26 multistriata 30 ) have become available in recent years, which allows the analysis of the evolutionary 27 history within diatoms. It is not fully understood how HGT has contributed to the ecological success of 28 this environmentally important group of organisms.…”

“…Although HGT detection has been previously performed in diatoms within the context of genome 32 projects 7,24,25,27,30 , they were based on different methodologies and criteria and are therefore not 33 directly comparable. While some studies used phylogenetics 7,30 , others relied purely on sequence 34 homology searches 24,25,27 . In this study, we sought to systematically detect HGT events simultaneously 35 across all sequenced diatoms.…”